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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcctcatgacttctattgttgaatttctgctgagtaacatttgtctgacaactgttcttggaacatttgcctttag

Basic information

species Zea mays
transcript GRMZM2G130889_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 13
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcctc--------------atgacttctattgttgaatttctgctgag---taacatttgtctgacaactgttcttg--gaacattt--gcctttag
  | |||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||| || || || |||||||||||| | ||  |               ||  | || ||  || |||| |  |||||   ||   |  | || |||    ||||||   || ||||  | ||  ||
TCTTACGGGGAACAAAACATACCAAGACTGGGGGTGGGACATATTCCAGGCATTTGAAAAGAACTCCCGCATAGAATCTGGTTACGTTGGGCTGAGAGATgtaagctttttttaattgtttttatgatagcatccatacttaaattcccactgagcgctagtgtaagacttacacaaattcttgtcaaatattttggtctccag

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G02290.1 (Glycine max), 5'ss of exon 12
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtagg-attcctca---tgacttctattgttgaatttctgctgag-----taacatttgtctgacaactgt----tcttggaacatttgcctttag----
  | || || || ||||| |||||||| ||||| ||| | ||||| || || ||||||||||||||||| ||||| || || ||||| |||||||  |||||| | |  |||||   | || |||| |  ||  ||| || | |      ||   ||| | ||  || |      | |   ||  |    | || |    
TCTAACTGGCAACAAAACGTACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGGATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcaaacctcaatttcacatctaataatgtgtttttgtttacattattattgtttctgtgtaaagtacatcctatcaaaagttagatcatttgttct

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtagg-attcctca---tgacttctattgttgaatttctgctga-------gtaacatttgtctgacaactgttct-tggaacatttgcct-ttag----
  | || || || |||||||||||||| ||||| ||| | ||||| || || ||||||||||||||||||||||| || || ||||| |||||||  |||||| | |  |||||   | || |||| |  ||  ||| || |          |    ||||| |||      | || |  ||  || |  | || |    
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagcacacctcaatttcacatctaataatgtgtttttgtttgcattattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 5'ss of exon 13
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc-------------tcatgacttctattgttgaatttctgctgagtaacatt-tgtctgacaactgttcttgg-aacatttgcctttag-------------------------------------
 || || || || || ||||| ||||| ||||| ||| | |||||  | ||||||||||||||||| |||||||| ||||||||||| ||  |||  |||||| | || |             | |   | |  |||||| ||    || ||| |   ||| | ||   | ||  |   |   |  | |||  | ||                                      
GTTAACTGGAAACAAGACATATCAAGAGTGGGGATGGAATATATTTGAAGCATTTGAGAAGAACTCGCGCATAGAGTCTGGATATGTTGGTTTGAAGGATgtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccag

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc--tca---tgacttctattgttga---atttctgctgagtaa-------catttgtctgacaactgttcttggaacatttgcctttag--------
 || || ||||| || ||||| ||||| ||||| ||| | ||||| || ||||||||||||||||| ||| |||||||||||||||| ||  |||  |||||| | |||    |    |||| |  |    | |   |        ||||         ||| | || || |   ||| ||  ||| ||||| | |          
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgtt--aacgtttgcttcttcattttcag

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 5'ss of exon 8
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtagg---attcctcatgacttctattgttgaatttctgctgagtaacatttgtctg-acaactgttcttggaacatttgcctttag-------------
 || || || |  || ||||||||||| ||||| ||| ||||||| || |||||||| ||||||||||||||||| || |||||||| |||||||  |||||| |   | || |||      ||| |    | ||    |||  | |  |   | |  |  | |    || |||| ||      |               
TTTAACTGGCAGCAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATATGTTGGACTGAAGGATgtaagtacactcttcaaactcactaatccctacttcagactggctgatttgcatttttagtatttacttttgaactttgattcctgaaatcttagaacat

upper sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 5'ss of exon 13
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtagg---attcctcatgacttctattgttgaatttctgctgagtaa--catttgtctgacaactgttcttggaacatttgcctttag-------------
 || || || || || ||||||||||| ||||| ||| ||||||| || |||||||| ||||||||||||||||| || ||||| || |||||||  |||||| |   | || |||      ||| |    | ||    |||| | |  |   | | |  ||  |  | ||| ||| ||      |               
TTTAACTGGCAACAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacactcttcaaactcactaatccctacttcagactgactgattcgcatttttagcatttacttttg-aactttgattcctgaaatcttagaaaat

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67028781|gb|CO457530.1|CO457530
EST:     ATTTGAGAAAGA-CTCCCGCATAGAATCTGGATACGTGGGACTGAGAGAT                         GTGAACACTGGNTGAAAAAGACA-CATGATGCAGAGTTTCTTCCTGGCAGA
genomic: ATTTGAGAA-GAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGG-TGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGA
EST: gi|8273174|gb|BE012264.1|BE012264
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|78112347|gb|DV530741.1|DV530741
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|60399791|gb|DN232601.1|DN232601
EST:     AACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: AACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|83278588|gb|DV942596.1|DV942596
EST:     GGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: GGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|8273156|gb|BE012247.1|BE012247
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|211104642|gb|FL379460.1|FL379460
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|13125955|gb|BG316630.1|BG316630
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|37392084|gb|CF633288.1|CF633288
EST:     GAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: GAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|21331268|gb|BQ486649.1|BQ486649
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|60291876|gb|DN190115.1|DN190115
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG
EST: gi|148928600|gb|EC873060.2|EC873060
EST:     CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGAT                         GTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCTTGGCAGAG
genomic: CATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT


Block sizes: 23 (upstream exon), 49 (downstream exon)
Score: 9

CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 29

CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 40

CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc ... ttgcctttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcctcatgacttctattgttgaatttctgctgagtaacatttgtctgacaactgttcttggaacatttgcctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC